About data processing:

Probe (cell) level data from the CEL file: These CEL values produced by MAS 5 are the 75% quantiles from a set of 36 pixel values per cell.

• Step 1: We added an offset of 1.0 to the CEL expression values for each cell to ensure that all values could be logged without generating negative values.
• Step 2: We took the log2 of each cell.
• Step 3: We computed the Z score for each cell.
• Step 4: We multiplied all Z scores by 2.
• Step 5: We added 8 to the value of all Z scores. The consequence of this simple set of transformations is to produce a set of Z scores that have a mean of 8, a variance of 4, and a standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression level corresponds approximately to a 1 unit difference.
• Step 6: We computed the arithmetic mean of the values for the set of microarrays for each of the individual strains.

Probe set data from the TXT file: These TXT files were generated using the MAS 5. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1-unit difference therefore represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.

About the array probe set names:

Most probe sets on the U74Av2 array consist of a total of 32 probes, divided into 16 perfect match probes and 16 mismatch controls. Each set of these 25-nucleotide-long probes has an identifier code that includes a unique number, an underscore character, and several suffix characters that highlight design features. The most common probe set suffix is at. This code indicates that the probes should hybridize relatively selectively with the complementary anti-sense target (i.e., the complemenary RNA) produced from a single gene. Other codes include:

• f_at (sequence family): Some probes in this probe set will hybridize to identical and/or slightly different sequences of related gene transcripts.
• s_at (similarity constraint): All Probes in this probe set target common sequences found in transcripts from several genes.
• g_at (common groups): Some probes in this set target identical sequences in multiple genes and some target unique sequences in the intended target gene.
• r_at (rules dropped): Probe sets for which it was not possible to pick a full set of unique probes using the Affymetrix probe selection rules. Probes were picked after dropping some of the selection rules.
• i_at (incomplete): Designates probe sets for which there are fewer than the standard numbers of unique probes specified in the design (16 perfect match for the U74Av2).
• st (sense target): Designates a sense target; almost always generated in error.

Descriptions for the probe set extensions were taken from the Affymetrix GeneChip Expression Analysis Fundamentals.